Fast tensor-based electrostatic energy calculations in the perspective of protein-ligand docking problem
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arXiv
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| Autori principali: | , , , |
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| Natura: | Preprint |
| Pubblicazione: |
2025
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| _version_ | 1866909878580150272 |
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| author | Benner, Peter Khoromskij, Boris N. Khoromskaia, Venera Stein, Matthias |
| author_facet | Benner, Peter Khoromskij, Boris N. Khoromskaia, Venera Stein, Matthias |
| contents | We propose and justify a new approach for fast calculation of the electrostatic interaction energy of clusters of charged particles in constrained energy minimization in the framework of rigid protein-ligand docking. Our ``blind search'' docking technique is based on the low-rank range-separated (RS) tensor-based representation of the free-space electrostatic potential of the biomolecule represented on large $n\times n\times n$ 3D grid. We show that both the collective electrostatic potential of a complex protein-ligand system and the respective electrostatic interaction energy can be calculated by tensor techniques in $O(n)$-complexity, such that the numerical cost for energy calculation only mildly (logarithmically) depends on the number of particles in the system. Moreover, tensor representation of the electrostatic potential enables usage of large 3D Cartesian grids (of the order of $n^3 \sim 10^{12}$), which could allow the accurate modeling of complexes with several large proteins. In our approach selection of the correct geometric pose predictions in the localized posing process is based on the control of van der Waals distance between the target molecular clusters. Here, we confine ourselves by constrained minimization of the energy functional by using only fast tensor-based free-space electrostatic energy recalculation for various rotations and translations of both clusters. Numerical tests of the electrostatic energy-based ``protein-ligand docking'' algorithm applied to synthetic and realistic input data present a proof of concept for rather complex particle configurations. The method may be used in the framework of the traditional stochastic or deterministic posing/docking techniques. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2510_26611 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Fast tensor-based electrostatic energy calculations in the perspective of protein-ligand docking problem Benner, Peter Khoromskij, Boris N. Khoromskaia, Venera Stein, Matthias Numerical Analysis 65F30, 65F50, 65N35, 65F10 We propose and justify a new approach for fast calculation of the electrostatic interaction energy of clusters of charged particles in constrained energy minimization in the framework of rigid protein-ligand docking. Our ``blind search'' docking technique is based on the low-rank range-separated (RS) tensor-based representation of the free-space electrostatic potential of the biomolecule represented on large $n\times n\times n$ 3D grid. We show that both the collective electrostatic potential of a complex protein-ligand system and the respective electrostatic interaction energy can be calculated by tensor techniques in $O(n)$-complexity, such that the numerical cost for energy calculation only mildly (logarithmically) depends on the number of particles in the system. Moreover, tensor representation of the electrostatic potential enables usage of large 3D Cartesian grids (of the order of $n^3 \sim 10^{12}$), which could allow the accurate modeling of complexes with several large proteins. In our approach selection of the correct geometric pose predictions in the localized posing process is based on the control of van der Waals distance between the target molecular clusters. Here, we confine ourselves by constrained minimization of the energy functional by using only fast tensor-based free-space electrostatic energy recalculation for various rotations and translations of both clusters. Numerical tests of the electrostatic energy-based ``protein-ligand docking'' algorithm applied to synthetic and realistic input data present a proof of concept for rather complex particle configurations. The method may be used in the framework of the traditional stochastic or deterministic posing/docking techniques. |
| title | Fast tensor-based electrostatic energy calculations in the perspective of protein-ligand docking problem |
| topic | Numerical Analysis 65F30, 65F50, 65N35, 65F10 |
| url | https://arxiv.org/abs/2510.26611 |